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Related Concept Videos

Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...

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Related Experiment Video

Updated: May 15, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

Modelling dynamics in protein crystal structures by ensemble refinement.

B Tom Burnley1, Pavel V Afonine, Paul D Adams

  • 1Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science , Utrecht University , Utrecht , The Netherlands.

Elife
|December 20, 2012
PubMed
Summary
This summary is machine-generated.

Protein dynamics are crucial for function, yet X-ray crystallography often provides static views. Ensemble refinement using molecular dynamics (MD) and translation-libration-screw (TLS) models captures these dynamics, improving structural models and revealing functional insights.

Keywords:
Nonecrystallographydynamicsfunctionproteinstructure

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Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
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Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

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Last Updated: May 15, 2026

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
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Published on: December 1, 2020

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip
10:45

Crystallization and Structural Determination of an Enzyme:Substrate Complex by Serial Crystallography in a Versatile Microfluidic Chip

Published on: March 20, 2021

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Single X-ray structures fail to capture essential protein dynamics.
  • Protein flexibility and motion are critical for biological function.

Purpose of the Study:

  • To develop and validate an ensemble refinement method for X-ray crystallography.
  • To better understand protein structure-dynamics-function relationships.

Main Methods:

  • Ensemble generation via time-averaged refinement.
  • Incorporation of molecular dynamics (MD) for local vibrations.
  • Application of translation-libration-screw (TLS) models for global disorder.
  • Refinement of 20 protein datasets at 1.1-3.1 Å resolution.

Main Results:

  • Ensemble models significantly improved crystallographic data fit (reduced R(free) by 0.3-4.9%).
  • Identified 'molten cores' in some proteins, suggesting roles in ligand binding and enzyme activity.
  • Observed order-disorder changes in HIV protease linked to ligand binding and entropy compensation.

Conclusions:

  • Ensemble refinement provides a more accurate representation of protein structures by including dynamics.
  • This approach enhances understanding of how protein motion influences biological activity.
  • Reveals mechanisms like entropy compensation in enzyme function.